Afghan officials are describing the fatal shooting of two boys as an accident carried out by Australian forces, although official confirmation over the involvement of Diggers is still to be made.

Officials in Kandahar said the brothers, aged 11 and 12, were collecting firewood with donkeys when they were shot dead by fire from a NATO helicopter on Thursday.

''The children were killed by Australian troops. It was a mistaken incident, not a deliberate one,'' Oruzgan provincial governor Amir Mohammad Akhundzada said.

Australian Defence Force chief David Hurley offered his condolences to the boys' family.

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''We deeply regret that the International Security Assistance Forces were responsible for the unintended death of two young Afghan boys during the operation,'' he said on Sunday.

Australian soldiers from the Special Operations Task Group were conducting a routine liaison patrol when the incident occurred. ''Australian personnel immediately reported the incident to Afghan government officials and military leaders in Oruzgan. It is premature to make any determination about how the incident occurred or who was responsible,'' General Hurley said.

The coalition's International Security Assistance Force expressed ''deep regret'' over the deaths.

Force commander Joseph Dunford said the troops fired on what they thought were insurgents in Oruzgan province, and killed the brothers by accident. ''I offer my personal apology and condolences to the family of the boys,'' he said. ''I am committed to ensuring we do the right thing for the families of those we harmed, as well as for the community in which they lived. We take full responsibility for this tragedy.''

A joint Afghan-coalition team visited the district of Shahidi Hassas on Saturday to investigate.

Fareed Ayal, a spokesman for the provincial police chief, said the helicopter had been hunting for Taliban by tracking their radio signals. ''There wasn't any engagement with the Taliban, it was just a mistake that they have killed the two boys at an area where they thought they detected a Taliban radio signal,'' he said.

Security in Oruzgan is being handed over to Afghan forces. Most of Australia's 1550 troops are based there, training Afghan soldiers before the withdrawal of coalition troops by the end of next year.

On Monday, Prime Minister Julia Gillard said that the deaths of the boys was a genuine tragedy.

''The loss of life is tragic. The impact on families is tragic and the impact on soldiers involved in the operation is tragic too,'' she told reporters in Sydney.

Ms Gillard could not provide any further details, saying that it took time to get all the facts of operational incidents clear.

She said in her own experience, ''the first reports you get of an operational matter are later clarified by subsequent information''.

The Prime Minister backed General Hurley and the media briefing about the incident.

''This is the Chief of the Defence Force being very proper and very appropriate, making sure that any facts that are released are right.''

Opposition Leader Tony Abbott says reports that Australian soldiers may have been responsible for the deaths of two children in Afghanistan are ''absolutely tragic''.

When asked about the allegations, Mr Abbott said civilian deaths were a ''horrible feature of war''.

''It is absolutely tragic, absolutely tragic whenever we get civilian casualties of war,'' he told reporters in Sydney on Sunday.